I was wondering if I went with a 3.5" lift, and 31" tires, would I need to get stronger or bigger brakes to account for the bigger tires?

Been plotting for years to mod my jeep, and I'm bout good to go (college kid with no money).

 

you'll be fine. you've already got the dual diaphragm booster and rear disc.

 

Your '96 ZJ should have 4-wheel disc brakes already. You can get better pads and you'll be good to go IMO.
Dan